Search results for " Match"

Accelerating metagenomic read classification on CUDA-enabled GPUs.

2016

Metagenomic sequencing studies are becoming increasingly popular with prominent examples including the sequencing of human microbiomes and diverse environments. A fundamental computational problem in this context is read classification; i.e. the assignment of each read to a taxonomic label. Due to the large number of reads produced by modern high-throughput sequencing technologies and the rapidly increasing number of available reference genomes software tools for fast and accurate metagenomic read classification are urgently needed. We present cuCLARK, a read-level classifier for CUDA-enabled GPUs, based on the fast and accurate classification of metagenomic sequences using reduced k-mers (…

Ultra-coarse-graining of homopolymers in inhomogeneous systems

2021

Abstract We develop coarse-grained (CG) models for simulating homopolymers in inhomogeneous systems, focusing on polymer films and droplets. If the CG polymers interact solely through two-body potentials, then the films and droplets either dissolve or collapse into small aggregates, depending on whether the effective polymer–polymer interactions have been determined from reference simulations in the bulk or at infinite dilution. To address this shortcoming, we include higher order interactions either through an additional three-body potential or a local density-dependent potential (LDP). We parameterize the two- and three-body potentials via force matching, and the LDP through relative entr…

Optimal Partitions of Strings: A New Class of Burrows-Wheeler Compression Algorithms

2003

The Burrows-Wheeler transform [1] is one of the mainstays of lossless data compression. In most cases, its output is fed to Move to Front or other variations of symbol ranking compression. One of the main open problems [2] is to establish whether Move to Front, or more in general symbol ranking compression, is an essential part of the compression process. We settle this question positively by providing a new class of Burrows-Wheeler algorithms that use optimal partitions of strings, rather than symbol ranking, for the additional step. Our technique is a quite surprising specialization to strings of partitioning techniques devised by Buchsbaum et al. [3] for two-dimensional table compression…

"Indexing structures for approximate string matching

2003

In this paper we give the first, to our knowledge, structures and corresponding algorithms for approximate indexing, by considering the Hamming distance, having the following properties. i) Their size is linear times a polylog of the size of the text on average. ii) For each pattern x, the time spent by our algorithms for finding the list occ(x) of all occurrences of a pattern x in the text, up to a certain distance, is proportional on average to |x| + |occ(x)|, under an additional but realistic hypothesis.

Third-harmonic generation in optical microfibers: From silica experiments to highly nonlinear glass prospects

2012

International audience; Using optical microfibers, phase matching between different propagation modes allows for third-harmonic generation (THG). After detailing the relevant phase matching conditions and overlap integrals, we provide a comparison between THG effective efficiencies in silica and tellurite glasses. We also explain the relatively easy, wideband, conversion that we observe experimentally in silica glass microfibers, from 155 mu m to the green, by the geometry of the tapering region.

Prospective associations of cardiovascular disease with physical performance and disability

2019

Background: Literature regarding cardiovascular disease (CVD) and incident physical performance limitations and disability in older people is equivocal. Aims: This study aimed to investigate whether CVD is longitudinally associated with incident physical performance limitations and disability in a large population-based sample. Methods: This was an 8‑year prospective study using data collected as part of the Osteoarthritis Initiative. Participants were community-dwelling adults with knee osteoarthritis or at high risk for this condition. Diagnosed CVD was self-reported. Physical performance was assessed with measures of chair stand time and gait speed, whereas disability was assessed with t…

Algoritmi di map matching per la ricostruzione dei percorsi stradali rilevati da dati GPS: aspetti teorici, computazionali e applicativi

2012

Hybrid Procedure for Automated Detection of Cracking with 3D Pavement Data

2016

Pavement cracks are considered a major indicator of pavement performance. Because traditional manual crack surveys are dangerous, time consuming, and expensive, technologies have been developed to collect high-speed pavement images, and numerous algorithms have been proposed to detect cracks on pavement surface. The latest PaveVision3D Ultra system (3D Ultra) has been implemented to achieve 30-kHz three-dimensional (3D) scanning rate for 1-mm resolution pavement surface data at highway speed up to 100 km/h (60  mi/h). This paper presents the application of a hybrid procedure for automated crack detection on 3D pavement data collected using 3D Ultra. The procedure combines three different me…

Relationship satisfaction can help to maintain the positive effect of childbirth on parental self-esteem

2020

The transition to parenthood is accompanied by declined self-esteem levels, which may be explained by parents’ relationship satisfaction. However, prior research examined self-esteem only shortly before and after childbirth and had no or only unmatched childless respondents as a control group, limiting the possibility to examine long-term adaptive processes and the causal interpretation of the associations. Thus, we used panel data (10 years, 4,075 individuals, and 16,122 observations) to compare self-esteem and relationship satisfaction trajectories of parents with matched childless respondents using propensity score matching. We found a quadratic trajectory for parents’ self-esteem, whic…

The Addition of Transarterial Chemoembolization to Palliative Chemotherapy Extends Survival in Intrahepatic Cholangiocarcinoma

2021

Incidence and mortality of intrahepatic cholangiocarcinoma (iCCA) have been increasing continuously. Recent studies suggest that the combination of palliative chemotherapy (pCTX) and transarterial chemoembolization (TACE) improves overall survival (OS). This study aimed to evaluate the outcome of patients treated with TACE and pCTX in unresectable iCCA at our tertiary care center. A group of 14 patients was treated with both pCTX and TACE. The non-randomized control group of 59 patients received pCTX alone. Patients received a median of two pCTX lines in both groups. Those treated with TACE underwent a median number of 3.5 sessions. Median OS from the time of unresectability was 26.2 months…